feat: Add foreign key on ecr_rr_conditions to the condition_reference table
#678
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #678 +/- ##
==========================================
+ Coverage 87.48% 92.24% +4.75%
==========================================
Files 268 164 -104
Lines 14101 7475 -6626
Branches 886 873 -13
==========================================
- Hits 12336 6895 -5441
+ Misses 1748 574 -1174
+ Partials 17 6 -11
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
akasper
force-pushed
the
akasper/condition-ref-fk
branch
from
aab819c to
d50d5c8
Compare
mcmcgrath13
reviewed
May 1, 2025
containers/ecr-viewer/src/app/api/migrate-db/migrations/core/20250430160000_condition_fk.ts
Outdated
Show resolved
Hide resolved
mcmcgrath13
reviewed
May 2, 2025
containers/ecr-viewer/src/app/api/migrate-db/migrations/core/20250430160000_condition_fk.ts
Outdated
Show resolved
Hide resolved
mcmcgrath13
reviewed
May 7, 2025
Comment on lines
312
to
319
| const rr_code = await trx | ||
| .selectFrom("condition_reference") | ||
| .select("code") | ||
| .where("condition_name", "=", rrItem.condition) | ||
| .executeTakeFirst(); | ||
|
|
||
| if (!rr_code) { | ||
| console.error(`Condition ${rrItem.condition} not found in condition_reference table`); |
There was a problem hiding this comment.
can we add this to the metadata instead? Our conditions reference comes from TRS, so we should be able to just add the code to the metadata schema and get it from the fhir bundle if it exists
There was a problem hiding this comment.
ECR Viewer side of things is properly set up but getting a little lost in the weeds of orchestration. Would you mind taking a look at what I've done with the schema changes in the message parser @mcmcgrath13
[pre-commit.ci] auto fixes from pre-commit hooks
[pre-commit.ci] auto fixes from pre-commit hooks
akasper
force-pushed
the
akasper/condition-ref-fk
branch
from
c1ca43d to
b4b5673
Compare
mcmcgrath13
reviewed
May 9, 2025
containers/ecr-viewer/src/app/api/migrate-db/migrations/core/index.ts
Outdated
Show resolved
Hide resolved
mcmcgrath13
reviewed
May 9, 2025
containers/ecr-viewer/src/app/api/migrate-db/migrations/core/20250430160000_condition_fk.ts
Outdated
Show resolved
Hide resolved
mcmcgrath13
reviewed
May 9, 2025
...ecr-viewer/src/app/api/migrate-db/migrations/core/20250506120000_backfill_condition_codes.ts
Outdated
Show resolved
Hide resolved
mcmcgrath13
reviewed
May 9, 2025
...ecr-viewer/src/app/api/migrate-db/migrations/core/20250506120000_backfill_condition_codes.ts
Outdated
Show resolved
Hide resolved
mcmcgrath13
reviewed
May 9, 2025
...ecr-viewer/src/app/api/migrate-db/migrations/core/20250506120000_backfill_condition_codes.ts
Outdated
Show resolved
Hide resolved
mcmcgrath13
reviewed
May 9, 2025
Comment on lines
312
to
316
| const rr_code = await trx | ||
| .selectFrom("condition_reference") | ||
| .select("code") | ||
| .where("condition_name", "=", rrItem.condition) | ||
| .executeTakeFirst(); |
There was a problem hiding this comment.
still needs to be sourced from the metadata data (and metadata parser updated to add it)
mcmcgrath13
reviewed
May 12, 2025
containers/ecr-viewer/src/app/api/migrate-db/migrations/core/20250509000000_condition_fk.ts
Show resolved
Hide resolved
mcmcgrath13
reviewed
May 12, 2025
| .where("condition_code", "is", null) | ||
| .execute(); | ||
| } else if (dbDialect() === "sqlserver") { | ||
| const rows = await _db |
There was a problem hiding this comment.
would this branch also work for postgres?
mcmcgrath13
reviewed
May 15, 2025
Comment on lines
62
to
69
| "condition_code": { | ||
| "fhir_path": "iif(Observation.valueCodeableConcept.text.exists(), Observation.valueCodeableConcept.text, Observation.valueCodeableConcept.coding.display)", | ||
| "data_type": "string", | ||
| "nullable": true, | ||
| "metadata": { | ||
| "category": "RR Reportability Information" | ||
| } | ||
| }, |
There was a problem hiding this comment.
move this up into the rr section and maybe just name code?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
PULL REQUEST
Now that we have a consistent identifier for conditions (via the
condition_referencetable), are add a foreign key reference to those conditions in our per-eCR reportability response conditions.Summary
condition_idtoecr_rr_conditions, as well as a foreign keyecr_rr_conditionsRelated Issue
Ticket #513
Acceptance Criteria
condition_idshould be added to theecr_rr_conditionstable (both schemas). It should be a foreign key tocondition_referenceecr_rr_conditionsit should be stamped with this ID if it can be determined